Open yoann-dufresne opened 5 years ago
You are right, there should be a description for every read simulator how to modify the config accordingly, and the way to do this for the wgsim simulator is particularly ugly. I will need to have a look at that.
Having said that, the way it should work right now (changing the following 4 options): readsim=tools/wgsim/wgsim error_profiles=. # CAMISIM expects a directory, but the option is not really required profile=0.0 # error-rate type=wgsim
How can we do the error-free or customized error rate with the art_illumina-2.3.6/art_illumina
read simulator?
Error-free can only be done with wgsim
(see my comment above for this). It should not make a difference whether you use ART
or wgsim
here.
For using the custom error profiles of ART
please have a look at this pull request which describes how to add and use you own trained error profile: https://github.com/CAMI-challenge/CAMISIM/pull/88
I'm trying to use CAMISIM to generate a big fastq file containing community reads with no error.
If I understand well, this is possible using wgsim read simulator with the option "errorfree" (I saw that in the code). So, I changed the config file with theses values : readsim=tools/wgsim/wgsim error_profiles=errorfree
But this is not that simple. CAMISIM wants a file as input for the error_profiles value. How can I change the values for a working pipeline ?
I think that it should be nice to have one or more wiki pages to explain the possible values in the config file.